Daisy got in as a clone/echo fighter, remember.
Echo fighters are different in that they take minimal extra work to include.
The character slot isn't Daisy's, it's Peach's and Daisy's just sharing it.
Waluigi, however, is in an unfortunate middle ground.
Since he doesn't have his own game, there's not really enough Waluigi content to draw from to create a full fighter moveset.
And at the same time, he's not similar enough to be anyone's Echo fighter – giving Waluigi the moveset of Luigi or Wario would just feel wrong and unfitting.

The Wii Fit Trainers have their entire moveset based off of the different poses and games in their series. The trainers played the main role of the personal assistants, guiding the player through the exercises.

The Ice Climbers came from an NES game older than Super Mario Bros. and their moves are based off of their game series, even if their moves aren’t derived entirely from their character. Ness never uses PK Fire/Freeze/Thunder in Earthbound, and Lucas doesn’t either.

The Miis were the avatar characters for the Wii, and there are many original games made around them; Miitopia, all the Mii Plaza games, the Wii Sports and Pilotwings serieses, etc. Also, I’m 98% sure their inclusion was just Nintendo’s way of saying “You want Goku in Smash? Make him yourself.”

I think the main issue with Waluigi as a fighter is that he’s never been a big focus in any game he’s in. He’s just a fill-in so Wario could have a tennis partner back in the N64 era. Daisy was in Super Mario Land, but even she’s just a Peach alt. Of course, I could be forgetting something big, and if I am, someone please call me out on it.

A much better case for Waluigi’s inclusion in Smash Bros., is Captain Falcon. He was given a moveset entirely from scratch. Yet Captain Falcon’s evolved to be the mascot of F-Zero, whereas Waluigi hasn’t had a single official game mainly centered around him. It really is a shame Waluigi’s just an assist trophy, but at least he's in Smash in SOME form. (Poor Crash.)